[CPN] Window for comments on proposal

Tue Jan 10 16:11:11 EST 2012

David, thanks for this.

Could I ask a naive question:  instead of deciding between "organism"
(which can be an individual) or "taxonomic unit" (which seems to be
something that people name), is there a problem with the general word
"lineage," which seems to represent what we're all about, that is,
genealogical entities?  Thx for any clarification.  -- kp

> Hi all,
>
> 2 things.
>
> First, yes, I think that we (CPN) should get this discussion going now.
> If you haven't taken the time to read the proposal yet, now is a good time
> - if you have, and would like to comment, great.  A couple folks have
> already - I've pasted that thread below.
>
> Second, Mike K. wrote:
>> I'd like to send out a link once the date on that page is changed.
> This is a great idea.  I've cc'd Torsten here, so that he can update the
> comment window on the web to Jan. 31.  Thanks, Torsten.
>
> Mike, will you please send a note to the society to make them aware of
> this.
>
> Best,
> Dave
>
>
> Mike Keesey: Oct 5.
>>
>>
>> I like the idea of removing the dependency on species from the code,
>> thus avoiding the "species problem". In the past I've advocated a
>> similar approach, where we deal in organisms rather than species.
>> However, since then I've realized there is also an "organism problem"!
>> That is, it's not always clear in biology what constitutes an
>> individual organism (think of slime molds, lichens, etc.).
>>
>> Now I think perhaps it is preferable to think of phylogeny in terms of
>> taxonomic units. A phylogeny is a directed, acyclic graph wherein the
>> nodes are taxonomic units and the [directed] edges are [immediate]
>> ancestor-descendant relationships. How units and relationships are
>> determined is beyond the purview of the code (just as taxonomy is
>> beyond the purview of the rank-based codes), but the code requires
>> them in order to be applied.
>>
>> So I would suggest that perhaps we use the phrase "taxonomic units"
>> (or, where clear, just "units") instead of "organisms", "populations",
>> "species", etc.
>>
>> I've written a document explaining this approach in nauseating detail:
>> http://namesonnodes.org/ns/math/2009/index.html
>>
>>> Art. 2.1: I agree with the proposal, though I like Keesey's "ancestral
>>> set"
>>> even better.
>>
>> More recently I've been using the term "cladogen":
>> http://namesonnodes.org/ns/math/2009/index.html#section-Cladogens
>> --
>> T. Michael Keesey
>> http://tmkeesey.net/
>
> David M., Oct 6:
>
>>>> I'll offer some preliminary thoughts as well.
>>>>
>>>> I like the idea of removing the dependency on species from the
>>>> code, thus avoiding the "species problem". In the past I've
>>>> advocated a similar approach, where we deal in organisms rather
>>>> than species. However, since then I've realized there is also an
>>>> "organism problem"! That is, it's not always clear in biology what
>>>> constitutes an individual organism (think of slime molds, lichens,
>>>> etc.).
>>
>> That's true, but the organism problem is much, much smaller than the
>> species problem! Cases where it could lead to actual trouble will be, at
>> most, so rare that we (the CPN) could easily deal with them on a
>> case-to-case basis.
>>
>>>> Now I think perhaps it is preferable to think of phylogeny in terms
>>>> of taxonomic units. A phylogeny is a directed, acyclic graph
>>>> wherein the nodes are taxonomic units and the [directed] edges are
>>>> [immediate] ancestor-descendant relationships. How units and
>>>> relationships are determined is beyond the purview of the code
>>>> (just as taxonomy is beyond the purview of the rank-based codes),
>>>> but the code requires them in order to be applied.
>>>>
>>>> So I would suggest that perhaps we use the phrase "taxonomic
>>>> units" (or, where clear, just "units") instead of "organisms",
>>>> "populations", "species", etc.
>>
>> This will be misunderstood to include "higher taxa".
>>
>>>> I've written a document explaining this approach in nauseating
>>>> detail: http://namesonnodes.org/ns/math/2009/index.html
>>
>> I'll try to read it sometime... :-]
>>
>>>>> Art. 2.1: I agree with the proposal, though I like Keesey's
>>>>> "ancestral set" even better.
>>>>
>>>> More recently I've been using the term "cladogen":
>>>> http://namesonnodes.org/ns/math/2009/index.html#section-Cladogens
>>
>> That's a nice word!
>
> Oct 6: Mike Keesey:
>> In response to the proposed revisions, I wrote:
>>
>>> I'll offer some preliminary thoughts as well.
>>>
>>> I like the idea of removing the dependency on species from the code,
>>> thus avoiding the "species problem". In the past I've advocated a
>>> similar approach, where we deal in organisms rather than species.
>>> However, since then I've realized there is also an "organism problem"!
>>> That is, it's not always clear in biology what constitutes an
>>> individual organism (think of slime molds, lichens, etc.).
>>>
>>> Now I think perhaps it is preferable to think of phylogeny in terms of
>>> taxonomic units. A phylogeny is a directed, acyclic graph wherein the
>>> nodes are taxonomic units and the [directed] edges are [immediate]
>>> ancestor-descendant relationships. How units and relationships are
>>> determined is beyond the purview of the code (just as taxonomy is
>>> beyond the purview of the rank-based codes), but the code requires
>>> them in order to be applied.
>>>
>>> So I would suggest that perhaps we use the phrase "taxonomic units"
>>> (or, where clear, just "units") instead of "organisms", "populations",
>>> "species", etc.
>>>
>>> I've written a document explaining this approach in nauseating detail:
>>> http://namesonnodes.org/ns/math/2009/index.html
>>
>> In response, David Marjanović wrote:
>>
>>> That's true, but the organism problem is much, much smaller than the
>>> species problem! Cases where it could lead to actual trouble will be,
>>> at
>>> most, so rare that we (the CPN) could easily deal with them on a
>>> case-to-case basis.
>>
>> Likely true, and, to be clear, I would definitely favor using
>> "organisms" over "species", even if my ultimate preference is
>> "[taxonomic] units".
>>
>>> This will be misunderstood to include "higher taxa".
>>
>> If a taxonomic unit in a phylogenetic hypothesis is a "higher taxon"
>> then that is actually what I mean!
>>
>> I see the process of phylogenetic nomenclature this way:
>>
>> 1) A researcher, using whatever criteria they desire, organizes the
>> relevant life forms into units.
>>
>> 2) The researcher, again using whatever criteria they desire,
>> hypothesizes ancestor-descendant relationships between the units. We
>> now have a phylogenetic hypothesis, which is a directed, acyclic graph
>> where the taxonomic units are the nodes (or vertices) and the
>> immediate ancestor-descendant relationships are the directed edges (or
>> arcs).
>>
>> 3) The researcher consults RegNum for definitions which are applicable
>> to the phylogenetic hypothesis. Definitions are applicable if their
>> specifiers indicate units or unions of units in the hypothesis. (A
>> specimen should generally indicate a single unit, a species is just a
>> proxy for its type specimen, and an apomorphy may indicate a union of
>> any number of units, as may the term "extant".)
>>
>> 4) The researcher applies these definitions. Definitions indicate
>> operations which yield either the empty set, an individual unit, or a
>> union of units, depending on the phylogenetic hypothesis.
>>
>> 5) The names associated with these definitions, under the PhyloCode,
>> may now be used to refer to the appropriate taxa yielded by the
>> definitions (under the phylogenetic hypothesis).
>>
>> So, for example, suppose we have a phylogenetic hypothesis where one
>> of the units is "Aves", and we seek to apply a definition which uses
>> the type specimen of _Vultur gryphus_ as a specifier. (Note that, per
>> Note 11.1.1, "When a species is cited as a specifier, the implicit
>> specifier is the type of that species name (if a type has been
>> designated) under the appropriate rank-based code.") Then, in that
>> context, the taxonomic unit "Aves" is indicated by that specifier
>> (never mind that it's a "higher taxon").
>>
>> You may ask, what happens if another specifier indicates the same
>> unit? E.g., how do we apply the definition of _Neognathae_ (the
>> branch-modified node-based clade stemming from the last common
>> ancestor of all extant members of the branch-based clade stemming from
>> the first ancestor of _Vultur gryphus_ not also ancestral to _Tinamus
>> major_ or _Struthio camelus_)? All three of the specifiers indicate
>> the same unit ("Aves"), so doesn't that definition yield the empty
>> set? The answer is, yes, *under that context*, _Neognathae_ is empty!
>> But the conclusion to be drawn from this isn't that there are no
>> neognathes *under any context*, rather that this particular context is
>> too coarse for a useful application of the definition.
>>
>> --
>> T. Michael Keesey
>> http://tmkeesey.net/
>
> _________________________________
> David C. Tank
> Assistant Professor & Director, Stillinger Herbarium
> University of Idaho
> 208.885.7033
> dtank at uidaho.edu
> http://www.phylodiversity.net/dtank/
>
> On Jan 10, 2012, at 6:18 AM, Cantino, Philip wrote:
>
>> The end of the month is fine with me.  Does anyone have any thoughts on
>> the question I sent the listserv Jan. 5?  My question was whether CPN
>> members are expected to comment by the end of the public comment period
>> or save our comments for the CPN discussion.
>>
>> Phil
>>
>>
>> On Jan 9, 2012, at 5:14 PM, Mike Keesey wrote:
>>
>>> On Thu, Jan 5, 2012 at 1:15 PM, Kevin Padian <kpadian at berkeley.edu>
>>> wrote:
>>>> I agree with Michel, and I think that the end of the month is a good
>>>> deadline.  How does the Committee propose to proceed at that point?
>>>> -- kp
>>>
>>> I agree that the deadline for comments should be extended at least
>>> until the end of this month. (I wouldn't mind an even later date, as
>>> long as it doesn't delay our own discussion on this list.)
>>>
>>> Does anyone disagree? I'd like to send out a link once the date on
>>> that page is changed.
>>>
>>> --
>>> T. Michael Keesey
>>> http://tmkeesey.net/
>>>
>>> _______________________________________________
>>> CPN mailing list
>>> CPN at listserv.ohio.edu
>>> http://listserv.ohio.edu/mailman/listinfo/cpn
>>
>>
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-- 
Kevin Padian
Department of Integrative Biology &
Museum of Paleontology
University of California, Berkeley CA 94720-3140
510-642-7434
http://www.ucmp.berkeley.edu/people/padian/home.php